comparison flexbar.xml @ 7:589b4866f537

Uploaded Flexbar galaxy tool definition file flexbar.xml
author jtilman
date Sun, 30 Dec 2012 18:44:15 -0500
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children 4cbf6c6d2f2b
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6:c0c9b43670d0 7:589b4866f537
1
2 <!-- Author: Johannes T. Roehr -->
3
4 <tool id="flexbar" name="Flexbar" version="2.3" force_history_refresh="True">
5
6 <description>flexible barcode and adapter removal</description>
7
8 <requirements>
9 <requirement type="binary" version="2.3">flexbar</requirement>
10 </requirements>
11
12 <version_command>flexbar --version</version_command>
13
14 <command interpreter="perl">
15
16 flexbar.pl flexbar
17
18 --threads 1
19
20 --reads $reads
21
22 #if $cReads2.select == "on":
23 #if $cReads2.reads2.ext == $reads.ext:
24 --reads2 $cReads2.reads2
25 #end if
26 #end if
27
28
29 #if $reads.ext == "fasta":
30 --format fasta
31 #end if
32 #if $reads.ext == "fastq":
33 --format fastq
34 #end if
35 #if $reads.ext == "fastqsanger":
36 --format fastq-sanger
37 #end if
38 #if $reads.ext == "fastqsolexa":
39 --format fastq-solexa
40 #end if
41 #if $reads.ext == "fastqillumina":
42 --format fastq-i1.3
43 #end if
44 #if $reads.ext == "csfasta":
45 --format csfasta
46 #end if
47 #if $reads.ext == "fastqcssanger":
48 --format csfastq
49 #end if
50
51
52 --max-uncalled $maxUncalled
53 --min-readlength $minReadLen
54
55 #if $trimEnds.select == "on":
56 --pre-trim-left $trimEnds.trimLeft
57 --pre-trim-right $trimEnds.trimRight
58 #end if
59
60 #if $cTrimPhred.select == "on":
61 --pre-trim-phred $cTrimPhred.trimPhred
62 #end if
63
64 #if $cTrimLen.select == "on":
65 --post-trim-length $cTrimLen.trimLen
66 #end if
67
68
69 #if $cBarcodes.select == "on":
70 --barcodes $cBarcodes.barcodes
71
72 #if $cBarcodes.cbReads.select == "yes":
73 --barcode-reads $cBarcodes.cbReads.bReads
74 #end if
75
76 #if $cBarcodes.cbReads.select == "no":
77 $cBarcodes.cbReads.bKeep
78 #end if
79
80 --barcode-trim-end $cBarcodes.bTrimEnd
81
82 #if $cBarcodes.cbTailLen.select == "yes":
83 --barcode-tail-length $cBarcodes.cbTailLen.bTailLen
84 #end if
85
86 #if $cBarcodes.cbMinOverlap.select == "yes":
87 --barcode-min-overlap $cBarcodes.cbMinOverlap.bMinOverlap
88 #end if
89
90 --barcode-threshold $cBarcodes.bThresh
91
92 #if $cBarcodes.cbAlignScores.select == "yes":
93 --barcode-match $bMatch
94 --barcode-mismatch $bMismatch
95 --barcode-gap $bGap
96 #end if
97
98 #end if
99
100
101 #if $cAdapters.select == "yes":
102
103 #if $cAdapters.ccAdapters.select == "data":
104 --adapters $cAdapters.ccAdapters.adaptersData
105 #end if
106
107 #if $cAdapters.ccAdapters.select == "seq":
108 --adapter-seq $cAdapters.ccAdapters.adapterSeq
109 #end if
110
111 --adapter-trim-end $cAdapters.aTrimEnd
112
113 #if $cAdapters.caTailLen.select == "yes":
114 --adapter-tail-length $cAdapters.caTailLen.aTailLen
115 #end if
116
117 --adapter-min-overlap $cAdapters.aMinOverlap
118 --adapter-threshold $cAdapters.aThresh
119
120 #if $cAdapters.caAlignScores.select == "on":
121 --adapter-match $aMatch
122 --adapter-mismatch $aMismatch
123 --adapter-gap $aGap
124 #end if
125
126 #end if
127
128
129 #if $cLogging.select == "show"
130 $cLogging.logLevel
131 $cLogging.noLenDist
132 $cLogging.remTag
133 #end if
134
135 #if $cLogging.select == "off"
136 --no-length-dist
137 #end if
138
139
140 $output $output.id $__new_file_path__ $reads.ext
141
142 </command>
143
144 <inputs>
145
146 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/>
147
148
149 <conditional name="cReads2">
150 <param name="select" type="select" label="2nd read set (paired)">
151 <option value="off" selected="true">Off</option>
152 <option value="on">On</option>
153 </param>
154 <when value="on">
155 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads2" type="data" label="Reads 2" optional="false" help="same format as first read set"/>
156 </when>
157 </conditional>
158
159
160 <param name="maxUncalled" size="4" type="integer" value="0" label="1) Max uncalled" optional="false" help="allowed uncalled bases per read"/>
161
162 <conditional name="trimEnds">
163 <param name="select" type="select" label="2) Trimming of ends">
164 <option value="off" selected="true">Off</option>
165 <option value="on">On</option>
166 </param>
167 <when value="on">
168 <param name="trimLeft" size="4" type="integer" value="0" label="Left" optional="false"/>
169 <param name="trimRight" size="4" type="integer" value="0" label="Right" optional="false" help="trims specified number of bases from read ends"/>
170 </when>
171 </conditional>
172
173 <conditional name="cTrimPhred">
174 <param name="select" type="select" label="3) Phred-trimming">
175 <option value="off" selected="true">Off</option>
176 <option value="on">On</option>
177 </param>
178 <when value="on">
179 <param name="trimPhred" size="4" type="integer" value="10" label="Threshold" optional="false" help="trim right end until specified or higher quality reached"/>
180 </when>
181 </conditional>
182
183
184 <conditional name="cBarcodes">
185 <param name="select" type="select" label="4) Barcode detection">
186 <option value="off" selected="true">Off</option>
187 <option value="on">On</option>
188 </param>
189 <when value="on">
190 <param format="fasta" name="barcodes" type="data" label="Barcodes" optional="false"/>
191 <conditional name="cbReads">
192 <param name="select" type="select" label="Separate barcode reads">
193 <option value="no" selected="true">No</option>
194 <option value="yes">Yes</option>
195 </param>
196 <when value="yes">
197 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="bReads" type="data" label="Separate barcode reads" optional="false"/>
198 </when>
199 <when value="no">
200 <param name="bKeep" type="select" label="Remove barcodes within reads">
201 <option value="" selected="true">Yes</option>
202 <option value="--barcode-keep">No</option>
203 </param>
204 </when>
205 </conditional>
206 <param name="bTrimEnd" type="select" label="Trim-end mode" optional="false">
207 <option value="ANY" selected="true">Any</option>
208 <option value="RIGHT">Right</option>
209 <option value="RIGHT_TAIL">Right tail</option>
210 <option value="LEFT">Left</option>
211 <option value="LEFT_TAIL">Left tail</option>
212 </param>
213 <conditional name="cbTailLen">
214 <param name="select" type="select" label="Change tail length">
215 <option value="no" selected="true">No</option>
216 <option value="yes">Yes</option>
217 </param>
218 <when value="yes">
219 <param name="bTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/>
220 </when>
221 </conditional>
222
223 <conditional name="cbMinOverlap">
224 <param name="select" type="select" label="Change min-overlap" help="default: barcode length">
225 <option value="no" selected="true">No</option>
226 <option value="yes">Yes</option>
227 </param>
228 <when value="yes">
229 <param name="bMinOverlap" size="4" type="integer" value="8" label="Min-overlap" optional="false"/>
230 </when>
231 </conditional>
232
233 <param name="bThresh" size="4" type="integer" value="1" label="Threshold" optional="false" help="allowed mismatches and indels per 10 bases"/>
234
235 <conditional name="cbAlignScores">
236 <param name="select" type="select" label="Modify alignment scores">
237 <option value="no" selected="true">No</option>
238 <option value="yes">Yes</option>
239 </param>
240 <when value="yes">
241 <param name="bMatch" size="3" type="integer" value="1" label="Match" optional="false"/>
242 <param name="bMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/>
243 <param name="bGap" size="3" type="integer" value="-7" label="Gap" optional="false"/>
244 </when>
245 </conditional>
246 </when>
247 </conditional>
248
249
250 <conditional name="cAdapters">
251 <param name="select" type="select" label="5) Adapter removal">
252 <option value="off" selected="true">Off</option>
253 <option value="on">On</option>
254 </param>
255
256 <when value="on">
257 <conditional name="ccAdapters">
258 <param name="select" type="select" label="Adapter source">
259 <option value="data" selected="true">Fasta</option>
260 <option value="seq">Sequence</option>
261 <!-- <option value="file">File</option> -->
262 </param>
263 <when value="data">
264 <param format="fasta" name="adaptersData" type="data" label="Adapters" optional="false"/>
265 </when>
266 <when value="seq">
267 <param name="adapterSeq" size="40" label="Adapter" type="text" value="AAAAAAAAAAAAAA" optional="false"/>
268 </when>
269 <!-- <when value="file">
270 <param name="adaptersFile" type="file" label="Adapters file" optional="false"/>
271 </when> -->
272 </conditional>
273
274 <param name="aTrimEnd" type="select" label="Trim-end mode" optional="false">
275 <option value="ANY">Any</option>
276 <option value="RIGHT" selected="true">Right</option>
277 <option value="RIGHT_TAIL">Right tail</option>
278 <option value="LEFT">Left</option>
279 <option value="LEFT_TAIL">Left tail</option>
280 </param>
281
282 <conditional name="caTailLen">
283 <param name="select" type="select" label="Change tail length">
284 <option value="no" selected="true">No</option>
285 <option value="yes">Yes</option>
286 </param>
287 <when value="yes">
288 <param name="aTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/>
289 </when>
290 </conditional>
291
292 <param name="aMinOverlap" size="4" type="integer" value="1" label="Min-overlap" optional="false"/>
293 <param name="aThresh" size="4" type="integer" value="3" label="Threshold" optional="false" help="allowed mismatches and indels per 10 bases"/>
294
295 <conditional name="caAlignScores">
296 <param name="select" type="select" label="Modify alignment scores">
297 <option value="no" selected="true">No</option>
298 <option value="yes">Yes</option>
299 </param>
300 <when value="yes">
301 <param name="aMatch" size="3" type="integer" value="1" label="Match" optional="false"/>
302 <param name="aMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/>
303 <param name="aGap" size="3" type="integer" value="-7" label="Gap" optional="false"/>
304 </when>
305 </conditional>
306 </when>
307 </conditional>
308
309
310 <conditional name="cTrimLen">
311 <param name="select" type="select" label="6) Trimming to length">
312 <option value="off" selected="true">Off</option>
313 <option value="on">On</option>
314 </param>
315 <when value="on">
316 <param name="trimLen" size="4" type="integer" value="30" label="Length" optional="false" help="trim reads to certain length from right"/>
317 </when>
318 </conditional>
319
320 <param name="minReadLen" size="4" type="integer" value="18" label="7) Minimum read length" optional="false" help="shorter reads are discarded"/>
321
322
323 <conditional name="cLogging">
324 <param name="select" type="select" label="Logging and tagging options">
325 <option value="off" selected="true">Off</option>
326 <option value="show">Show</option>
327 </param>
328 <when value="show">
329 <param name="logLevel" type="select" label="Alignment logging">
330 <option value="" selected="true">Off</option>
331 <option value="--log-level ALL">All</option>
332 <option value="--log-level MOD">Modified</option>
333 <option value="--log-level TAB">Tabular</option>
334 </param>
335
336 <param name="noLenDist" type="select" label="Read length distribution">
337 <option value="--no-length-dist" selected="true">Off</option>
338 <option value="">On</option>
339 </param>
340
341 <param name="remTag" type="select" label="Read tagging">
342 <option value="" selected="true">Off</option>
343 <option value="--removal-tag">Removal tags</option>
344 </param>
345 </when>
346 </conditional>
347
348 </inputs>
349
350 <stdio>
351 <exit_code range="1:" level="fatal" description="Error!" />
352 </stdio>
353
354 <outputs>
355 <data format="txt" name="output" metadata_source="reads"/>
356 </outputs>
357
358
359 <help>
360 **Flexbar help**
361
362 Flexbar_ is a program to preprocess sequencing data. It demultiplexes barcoded runs and removes adapter sequences. Further, basic read trimming and filtering options are provided. Flexbar increases mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform.
363
364 .. _Flexbar: https://sourceforge.net/projects/flexbar
365
366 ------
367
368 **Reference**
369
370 Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar — flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012, 1(3):895-905.
371
372 ------
373
374 **Trim-end modes**
375
376 **Any:** longer part of read remains
377
378 **Left:** align before or at read end, right part remains
379
380 **Right:** align after or at read start, left part remains
381
382 **Left tail:** consider first n bases, see tail-length options
383
384 **Right tail:** use only last n bases of reads in alignment
385
386 ------
387
388 **Documentation**
389
390 .. class:: warningmark
391
392 Further documentation is available on the `manual`__ wiki and via the command line help screen.
393
394 .. __: http://sourceforge.net/p/flexbar/wiki
395 </help>
396
397 </tool>
398